Re: [Matplotlib-users] netcdf4-python build

2012-09-21 Thread Michael Rawlins 





>
> From: Damon McDougall 
>To: Michael Rawlins  
>Cc: "matplotlib-users@lists.sourceforge.net" 
> 
>Sent: Friday, September 21, 2012 2:50 PM
>Subject: Re: [Matplotlib-users] netcdf4-python build
> 
>
>
>
>From what I remember dealing with the netcdf c library, you have to explicitly 
>set a compile flag to enable hdf5 support. That was a while ago, though. I'm 
>not sure if things have changed.
>
>
>Hope this helps.
>
>
>
>
>I did not do a source compile. 
>
>I've reinstalled libhdf5-serial-1.8.4 package and now have the right HDF5 
>library files. Successfully built and installed netCDF4-1.0.  My script loads 
>in module but a read/write issue is present. This is code that worked on 
>previous system. Error:
>
>  File "test.py", line 96, in 
>    data.missing_value=-9.99
>  File "netCDF4.pyx", line 2570, in netCDF4.Variable.__setattr__ 
>(netCDF4.c:28242)
>  File "netCDF4.pyx", line 2392, in netCDF4.Variable.setncattr 
>(netCDF4.c:26309)
>  File "netCDF4.pyx", line 1013, in netCDF4._set_att (netCDF4.c:12699)
>AttributeError: NetCDF: Write to read only
>
>
>The statement in the code triggers the error.
>
>data.missing_value=-9.99 .
>
>MR
>--
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Re: [Matplotlib-users] netcdf4-python build

2012-09-21 Thread Damon McDougall 
On Friday, September 21, 2012, Michael Rawlins wrote:

>
> After the build, I determined that 'install' was also needed.
>
> > python setup.py install
>
> completed with no errors.  OK, finally built and installed. But now my
> matplotlib script gives this error:
>
> Traceback (most recent call last):
>   File "map_PrcpBias_Northeast.py", line 21, in 
> from netCDF4 import Dataset as NetCDFFile
> ImportError: /usr/local/lib/python2.7/dist-packages/netCDF4.so: undefined
> symbol: nc_inq_var_endian
>
>
> So, checking shared library dependencies:
>
> > ldd /usr/local/lib/python2.7/dist-packages/netCDF4.so
>
> linux-gate.so.1 =>  (0xb776a000)
> libnetcdf.so.7 => /usr/local/lib/libnetcdf.so.7 (0xb7604000)
> libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0xb75d3000)
> libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb742d000)
> libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7401000)
> /lib/ld-linux.so.2 (0xb776b000)
>
> and
>
> > ldd /usr/local/lib/libnetcdf.so.7
>
> linux-gate.so.1 =>  (0xb7765000)
> libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7663000)
> libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb74be000)
> /lib/ld-linux.so.2 (0xb7766000)
>
> no libhdf5 there. Can this be fixed?
>
> MR
>
>
>
>
>From what I remember dealing with the netcdf c library, you have to
explicitly set a compile flag to enable hdf5 support. That was a while ago,
though. I'm not sure if things have changed.

Hope this helps.


-- 
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Re: [Matplotlib-users] netcdf4-python build

2012-09-21 Thread Michael Rawlins 

After the build, I determined that 'install' was also needed.

> python setup.py install

completed with no errors.  OK, finally built and installed. But now my 
matplotlib script gives this error:

Traceback (most recent call last):
  File "map_PrcpBias_Northeast.py", line 21, in 
    from netCDF4 import Dataset as NetCDFFile 
ImportError: /usr/local/lib/python2.7/dist-packages/netCDF4.so: undefined 
symbol: nc_inq_var_endian


So, checking shared library dependencies:

> ldd /usr/local/lib/python2.7/dist-packages/netCDF4.so

    linux-gate.so.1 =>  (0xb776a000)
    libnetcdf.so.7 => /usr/local/lib/libnetcdf.so.7 (0xb7604000)
    libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0xb75d3000)
    libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb742d000)
    libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7401000)
    /lib/ld-linux.so.2 (0xb776b000)

and

> ldd /usr/local/lib/libnetcdf.so.7

    linux-gate.so.1 =>  (0xb7765000)
    libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7663000)
    libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb74be000)
    /lib/ld-linux.so.2 (0xb7766000)

no libhdf5 there. Can this be fixed?

MR--
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Re: [Matplotlib-users] netcdf4-python build

2012-09-19 Thread Michael Rawlins 



>
> From: Jeff Whitaker 
>To: Michael Rawlins  
>Cc: "matplotlib-users@lists.sourceforge.net" 
> 
>Sent: Wednesday, September 19, 2012 5:57 PM
>Subject: Re: [Matplotlib-users] netcdf4-python build
> 
>
>On 9/19/12 3:29 PM, Michael Rawlins wrote:
>
>
>>
>>How is full traceback obtained?
>>>
>Michael:  I just meant for you to paste the full output, not just
the first three lines.
>
>
>That's all that appears at standard output and I do not know how to 
>generate/find anything else.
>
>
>Since you apparently have all the libs installed, I don't understand
what's going on.  Please try deleting the netcdf4-python build
directory, and then run 'python setup.py build' again, capturing the
output in a file.  Send me that file off-list and I'll see if I can
suggest something.
>
>-Jeff
>
>
>Out of build, after removing build/ directory:
>
>HDF5_DIR environment variable not set, checking some standard locations ..
>checking /home/rawlins ...
>checking /usr/local ...
>HDF5 found in /usr/local
>
>NETCDF4_DIR environment variable not set, checking standard locations.. 
>checking /home/rawlins ...
>checking /usr/local ...
>netCDF4 found in /usr/local
>running build
>running config_cc
>unifing config_cc, config, build_clib, build_ext, build commands --compiler 
>opti
>ons
>running config_fc
>unifing config_fc, config, build_clib, build_ext, build commands --fcompiler 
>opt
>ions
>running build_src
>build_src
>building py_modules sources
>building extension "netCDF4" sources
>build_src: building npy-pkg config files
>running build_py
>creating build
>creating build/lib.linux-i686-2.7
>copying netcdftime.py -> build/lib.linux-i686-2.7
>copying netCDF4_utils.py -> build/lib.linux-i686-2.7
>copying ordereddict.py -> build/lib.linux-i686-2.7
>running build_ext
>customize UnixCCompiler
>customize UnixCCompiler using build_ext
>building 'netCDF4' extension
>compiling C sources
>C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall 
>-Wst
>rict-prototypes -fPIC
>
>creating build/temp.linux-i686-2.7
>compile options: '-I/usr/local/include -I/usr/local/include 
>-I/usr/lib/python2.7
>/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
>gcc: netCDF4.c
>netCDF4.c: In function '__pyx_f_7netCDF4__find_cmptype':
>netCDF4.c:46724:13: warning: '__pyx_v_xtype' may be used uninitialized in this 
>f
>unction [-Wuninitialized]
>netCDF4.c:37881:11: note: '__pyx_v_xtype' was declared here
>gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions 
>-
>Wl,-z,relro build/temp.linux-i686-2.7/netCDF4.o -L/usr/local/lib 
>-L/usr/local/li
>b -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lz -o 
>bui
>ld/lib.linux-i686-2.7/netCDF4.so
>running scons
>running build_scripts
>creating build/scripts.linux-i686-2.7
>copying and adjusting utils/nc3tonc4 -> build/scripts.linux-i686-2.7
>copying and adjusting utils/nc4tonc3 -> build/scripts.linux-i686-2.7
>changing mode of build/scripts.linux-i686-2.7/nc3tonc4 from 644 to 755
>changing mode of build/scripts.linux-i686-2.7/nc4tonc3 from 644 to 755
>
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Re: [Matplotlib-users] netcdf4-python build

2012-09-19 Thread Jeff Whitaker 

On 9/19/12 3:29 PM, Michael Rawlins wrote:




*From:* Jeff Whitaker 
*To:* Michael Rawlins 
*Sent:* Wednesday, September 19, 2012 4:57 PM
*Subject:* Re: [Matplotlib-users] netcdf4-python build

On 9/19/12 2:43 PM, Michael Rawlins wrote:




*From:* Johann Rohwer  <mailto:j...@sun.ac.za>
*To:* matplotlib-users@lists.sourceforge.net
<mailto:matplotlib-users@lists.sourceforge.net>
*Sent:* Wednesday, September 19, 2012 3:22 PM
*Subject:* Re: [Matplotlib-users] netcdf4-python build

On 19/09/2012 21:14, Michael Rawlins wrote:

> Just installed h5utils from package manager. Getting same
errors.  In
> package manager I'm searching on hdf5. If there's a package
there I'm
> missing, then it certainly is not obvious.

Try

libhdf5-serial
libhdf5-serial-dev
Johann



After installing those two packages I was able build with
setup.py <http://setup.py/> in netCDF4-1.0/

Last few lines of the build:

creating build/scripts.linux-i686-2.7
copying and adjusting utils/nc3tonc4 -> build/scripts.linux-i686-2.7
copying and adjusting utils/nc4tonc3 -> build/scripts.linux-i686-2.7
changing mode of build/scripts.linux-i686-2.7/nc3tonc4 from 644
to 755
changing mode of build/scripts.linux-i686-2.7/nc4tonc3 from 644
to 755


Here is my initialization:

from mpl_toolkits.basemap import Basemap, shiftgrid, cm
from netCDF4 import Dataset as NetCDFFile

Here is result of execution of script:

Traceback (most recent call last):
  File "map_PrcpBias_Northeast.py
<http://map_prcpbias_northeast.py/>", line 21, in 
from netCDF4 import Dataset as NetCDFFile


Michael:  Please include the full traceback - what you posted
doesn't really tell us anything.


How is full traceback obtained?



Michael:  I just meant for you to paste the full output, not just the 
first three lines.


Since you apparently have all the libs installed, I don't understand 
what's going on.  Please try deleting the netcdf4-python build 
directory, and then run 'python setup.py build' again, capturing the 
output in a file.  Send me that file off-list and I'll see if I can 
suggest something.


-Jeff






I understand using the python-netcdf package is an option.
Installed that but am getting an eror saying missing
libhdf5_hl.so.6 when trying:

Do you have libhdf5_hl.so anywhere on your system after installing
the libhdf5-serial package? According to this

http://packages.ubuntu.com/lucid/i386/libhdf5-serial-1.8.4/filelist

it should be installed in /usr/lib.


Yes it is in /usr/lib.


Also, if I read this

http://packages.ubuntu.com/natty/libnetcdf6

correctly, just installing the libnetcdf6 and libnetcdf-dev
packages should be all you need to do - they depend on libhdf5-serial.

-Jeff


Both packages are installed.

MR



from Scientific.IO <http://scientific.io.net/>.NetCDF import
NetCDFFile

MR




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Re: [Matplotlib-users] netcdf4-python build

2012-09-19 Thread Michael Rawlins 





>
> From: Jeff Whitaker 
>To: Michael Rawlins  
>Sent: Wednesday, September 19, 2012 4:57 PM
>Subject: Re: [Matplotlib-users] netcdf4-python build
> 
>
>On 9/19/12 2:43 PM, Michael Rawlins wrote:
>
>
>>
>>
>>
>>
>>
>> From: Johann Rohwer 
>>To: matplotlib-users@lists.sourceforge.net 
>>Sent: Wednesday, September 19, 2012 3:22 PM
>>Subject: Re: [Matplotlib-users] netcdf4-python build
>> 
>>On 19/09/2012 21:14, Michael Rawlins wrote:
>>
>>> Just installed h5utils from package manager. Getting
same errors.  In
>>> package manager I'm searching on hdf5.  If there's a
package there I'm
>>> missing, then it certainly is not obvious.
>>
>>Try
>>
>>libhdf5-serial
>>libhdf5-serial-dev
>>Johann
>>
>>
>>
>>After installing those two packages I was able build with setup.py in 
>>netCDF4-1.0/
>>
>>Last few lines of the build:
>>
>>creating build/scripts.linux-i686-2.7
>>copying and adjusting utils/nc3tonc4 ->
build/scripts.linux-i686-2.7
>>copying and adjusting utils/nc4tonc3 ->
build/scripts.linux-i686-2.7
>>changing mode of build/scripts.linux-i686-2.7/nc3tonc4 from
644 to 755
>>changing mode of build/scripts.linux-i686-2.7/nc4tonc3 from
644 to 755
>>
>>
>>Here is my initialization:
>>
>>from mpl_toolkits.basemap import Basemap, shiftgrid, cm 
>>from netCDF4 import Dataset as NetCDFFile
>>
>>Here is result of execution of script:
>>
>>Traceback (most recent call last):
>>  File "map_PrcpBias_Northeast.py", line 21, in 
>>    from netCDF4 import Dataset as NetCDFFile 
>>
>Michael:  Please include the full traceback - what you posted
doesn't really tell us anything.
>
>
>How is full traceback obtained?
>
>
>
>
>>I understand using the python-netcdf package is an option.
Installed that but am getting an eror saying missing
libhdf5_hl.so.6 when trying:
>>
Do you have libhdf5_hl.so anywhere on your system after installing the 
libhdf5-serial package?  According to this
>
>http://packages.ubuntu.com/lucid/i386/libhdf5-serial-1.8.4/filelist
>
>it should be installed in /usr/lib.
>
>
>Yes it is in /usr/lib.
>
>
>Also, if I read this
>
>http://packages.ubuntu.com/natty/libnetcdf6
>
>correctly, just installing the libnetcdf6 and libnetcdf-dev packages
should be all you need to do - they depend on libhdf5-serial.
>
>-Jeff
>
>
>Both packages are installed.
>
>MR
>
>
>
>>from Scientific.IO.NetCDF import NetCDFFile
>>
>>MR
>>
>>
>>
>>--
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security and 
>>threat landscape has changed and how IT managers can
respond. Discussions 
>>will include endpoint security, mobile security and the
latest in malware 
>>threats.
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>>___
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>>https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>>
>>
>>
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>>
>>
>>___
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>
>
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Meteorologist   FAX: (303)497-6449
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 Office : Skaggs Research Cntr 1D-113
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>
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Re: [Matplotlib-users] netcdf4-python build

2012-09-19 Thread Michael Rawlins 





 From: Johann Rohwer 
To: matplotlib-users@lists.sourceforge.net 
Sent: Wednesday, September 19, 2012 3:22 PM
Subject: Re: [Matplotlib-users] netcdf4-python build
 
On 19/09/2012 21:14, Michael Rawlins wrote:

> Just installed h5utils from package manager. Getting same errors.  In
> package manager I'm searching on hdf5.  If there's a package there I'm
> missing, then it certainly is not obvious.

Try

libhdf5-serial
libhdf5-serial-dev
Johann



After installing those two packages I was able build with setup.py in 
netCDF4-1.0/

Last few lines of the build:

creating build/scripts.linux-i686-2.7
copying and adjusting utils/nc3tonc4 -> build/scripts.linux-i686-2.7
copying and adjusting utils/nc4tonc3 -> build/scripts.linux-i686-2.7
changing mode of build/scripts.linux-i686-2.7/nc3tonc4 from 644 to 755
changing mode of build/scripts.linux-i686-2.7/nc4tonc3 from 644 to 755


Here is my initialization:

from mpl_toolkits.basemap import Basemap, shiftgrid, cm 
from netCDF4 import Dataset as NetCDFFile

Here is result of execution of script:

Traceback (most recent call last):
  File "map_PrcpBias_Northeast.py", line 21, in 
    from netCDF4 import Dataset as NetCDFFile 

I understand using the python-netcdf package is an option. Installed that but 
am getting an eror saying missing libhdf5_hl.so.6 when trying:

from Scientific.IO.NetCDF import NetCDFFile

MR



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Re: [Matplotlib-users] netcdf4-python build

2012-09-19 Thread Johann Rohwer 
On 19/09/2012 21:14, Michael Rawlins wrote:

> Just installed h5utils from package manager. Getting same errors.  In
> package manager I'm searching on hdf5.  If there's a package there I'm
> missing, then it certainly is not obvious.

Try

libhdf5-serial
libhdf5-serial-dev
Johann

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Re: [Matplotlib-users] netcdf4-python build

2012-09-19 Thread Michael Rawlins 





 From: Jeff Whitaker 
To: Michael Rawlins ; Matplotlib Users 
 
Sent: Wednesday, September 19, 2012 2:35 PM
Subject: Re: [Matplotlib-users] netcdf4-python build
 

On 9/19/12 11:30 AM, Michael Rawlins wrote:


>
>Ubuntu 12.04
>
>
>hdf5-tools installed from package manager
>
>
>netcdf-bin and python-netcdf installed from package manager
>
>
>I downloaded netCDF4-1.0fix1.tar.gz from 
>http://code.google.com/p/netcdf4-python/downloads/list
>
>
>> python setup.py build
>
>
>
>
>/usr/bin/ld: cannot find -lhdf5_hl
>/usr/bin/ld: cannot find -lhdf5
>collect2: ld returned 1 exit status
>/usr/bin/ld: cannot find -lhdf5_hl
>/usr/bin/ld: cannot find -lhdf5
>collect2: ld returned 1 exit status
>error: Command "gcc -pthread -shared -Wl,-O1
  -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro
  build/temp.linux-i686-2.7/netCDF4.o -L/usr/local/lib
  -L/usr/local/lib -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib
  -lnetcdf -lhdf5_hl -lhdf5 -lz -o
  build/lib.linux-i686-2.7/netCDF4.so" failed with exit status 1
>
>
>
Michael:  You're missing the hdf5 library.  You should be able to
install that (along with the netcdf version 4 library) using the
Ubuntu package manager. I don't know what the relevant package names
are.

See the docs at netcdf4-python.googlecode.com for installation instructions 
(including how to install the dependencies).  

You can also file a help request there and I'll see it (since this
is not really a basemap issue).

-Jeff


Just installed h5utils from package manager. Getting same errors.  In package 
manager I'm searching on hdf5.  If there's a package there I'm missing, then it 
certainly is not obvious.

Mike


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Re: [Matplotlib-users] netcdf4-python build

2012-09-19 Thread Jeff Whitaker 

On 9/19/12 11:30 AM, Michael Rawlins wrote:


Ubuntu 12.04

hdf5-tools installed from package manager

netcdf-bin and python-netcdf installed from package manager

I downloaded netCDF4-1.0fix1.tar.gz 
 
from http://code.google.com/p/netcdf4-python/downloads/list


> python setup.py build


/usr/bin/ld: cannot find -lhdf5_hl
/usr/bin/ld: cannot find -lhdf5
collect2: ld returned 1 exit status
/usr/bin/ld: cannot find -lhdf5_hl
/usr/bin/ld: cannot find -lhdf5
collect2: ld returned 1 exit status
error: Command "gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions 
-Wl,-Bsymbolic-functions -Wl,-z,relro 
build/temp.linux-i686-2.7/netCDF4.o -L/usr/local/lib -L/usr/local/lib 
-Wl,-R/usr/local/lib -Wl,-R/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 
-lz -o build/lib.linux-i686-2.7/netCDF4.so" failed with exit status 1





Michael:  You're missing the hdf5 library.  You should be able to 
install that (along with the netcdf version 4 library) using the Ubuntu 
package manager. I don't know what the relevant package names are.


See the docs at netcdf4-python.googlecode.com for installation 
instructions (including how to install the dependencies).


You can also file a help request there and I'll see it (since this is 
not really a basemap issue).


-Jeff

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[Matplotlib-users] netcdf4-python build

2012-09-19 Thread Michael Rawlins 


Ubuntu 12.04

hdf5-tools installed from package manager

netcdf-bin and python-netcdf installed from package manager

I downloaded netCDF4-1.0fix1.tar.gz from 
http://code.google.com/p/netcdf4-python/downloads/list

> python setup.py build


/usr/bin/ld: cannot find -lhdf5_hl
/usr/bin/ld: cannot find -lhdf5
collect2: ld returned 1 exit status
/usr/bin/ld: cannot find -lhdf5_hl
/usr/bin/ld: cannot find -lhdf5
collect2: ld returned 1 exit status
error: Command "gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions 
-Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-i686-2.7/netCDF4.o 
-L/usr/local/lib -L/usr/local/lib -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib 
-lnetcdf -lhdf5_hl -lhdf5 -lz -o build/lib.linux-i686-2.7/netCDF4.so" failed 
with exit status 1--
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